GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Phaeobacter inhibens BS107

Align MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate GFF774 PGA1_c07880 alpha-glucoside transport system permease protein AglG

Query= TCDB::Q8DT26
         (278 letters)



>FitnessBrowser__Phaeo:GFF774
          Length = 382

 Score =  105 bits (262), Expect = 2e-27
 Identities = 70/240 (29%), Positives = 119/240 (49%), Gaps = 4/240 (1%)

Query: 42  YVPYIIPKTWTLDNY--IKLFTNSSFPFGRWFLNTLIVSTATCVLSTSITVAMAYSLSRI 99
           +V   +P  +TL+NY  + +  NS+    + F NTL V+    ++   +    AY+L+ +
Sbjct: 144 FVTATVPPEFTLENYETVLISGNSTDNMAKAFFNTLTVTIPATIIPILVAAFAAYALAWM 203

Query: 100 KFKHRNGFLKLALVLNMFPGFMSMIAVYYILKALNLTQTLTSLVLVYSS-GAALTFYIAK 158
           +F  R   +   + L + P  +++I +      + + +    + + ++  G  L  Y+ +
Sbjct: 204 EFPGRALLVAAIVGLLVVPLQLALIPLLKFHNEIGIGKGYIGVWMAHTGFGLPLAIYLLR 263

Query: 159 GFFDTIPYSLDESAMIDGATRKDIFLKITLPLSKPIIVYTALLAFIAPWIDFIFAQVILG 218
            +   IP  + E+A +DGAT   IF++I LPLS P +   A+  F+  W D + A V L 
Sbjct: 264 NYMVGIPRDIIENARVDGATDFLIFVRIILPLSFPALASFAIFQFLWTWNDLLVAMVFLI 323

Query: 219 DATSKYTVAIGLFSMLQADTINNWFMAFAAGSVLIAIPITILFIFMQKYYVEGITGGSVK 278
           DAT + TV       L      NW +   +  V IA+P+ + F  MQKY V G+  GSVK
Sbjct: 324 DATGETTVMTKQIVELLGTRGGNWEILATSAFVSIAVPLAVFFA-MQKYLVRGLLAGSVK 382



 Score = 26.9 bits (58), Expect = 7e-04
 Identities = 11/33 (33%), Positives = 22/33 (66%)

Query: 4  KKQLQIGSIYALLILLSFIWLFPIIWVILTSFR 36
          +K   I ++   ++LL  +WLFP + ++++SFR
Sbjct: 7  EKPALIWALRLSVVLLVGLWLFPTLGLLVSSFR 39


Lambda     K      H
   0.330    0.142    0.428 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 287
Number of extensions: 18
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 278
Length of database: 382
Length adjustment: 28
Effective length of query: 250
Effective length of database: 354
Effective search space:    88500
Effective search space used:    88500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory